## [1] "O76_p2_con_R1_2.hicup.bam"

Truncation & Mapping

Truncation Frequency

Category Read 1 Read 2
Total 79,798,526 79,798,526
Not Truncated 47,325,884 45,444,772
Truncated 32,472,642 34,353,754

Truncated Read Length

Category Read 1 Read 2
Average Length Truncated 46.7 45.5

Mapping Efficiency

Category Read 1 Read 2
Too Short To Map 5,055,767 6,668,530
Unique Alignments 68,792,703 65,684,615
Multiple Alignments 2,830,524 2,814,942
Failed To Align 3,119,532 4,630,439
Paired 57,256,244 57,256,244

Truncation and Mapping Bar Plot

Filtering

Filtering Breakdown by Category

Category Count
Valid Pairs 28,644,437
Invalid Pairs 28,611,807
Same Circularised 39,369
Same Dangling Ends 2,882,646
Same Fragment Internal 12,270,527
Re Ligation 11,367,397
Contiguous Sequence 301,278
Wrong Size 1,750,590
Total Pairs 57,256,244

Filtering Breakdown Pie Chart

Ditag Length Distribution

Frequency Line Plot

Deduplication

Deduplication Summary Table

Category All Ditags Unique Ditags
Read Pairs 28,644,437 41,137
Cis-close (<10Kbp) 2,604,284 3,862
Cis-far (>10Kbp) 19,851,079 22,948
Trans 6,189,074 14,327

Deduplication Bar Chart

Analysis produced by HiCUP - a tool for mapping and performing quality control on Hi-C data

Babraham Bioinformatics